Different scoring matrices

PAM
The first PAM matrix (Point Accepted Mutation) was published in 1978 by Dayhoff et al. The PAM matrix was build through a global alignment of related sequences all having sequence similarity above 85% [Dayhoff and Schwartz, 1978]. A PAM matrix shows the probability that any given amino acid will mutate into another in a given time interval. As an example, PAM1 gives that one amino acid out of a 100 will mutate in a given time interval. In the other end of the scale, a PAM256 matrix, gives the probability of 256 mutations in a 100 amino acids (see figure 14.13).

There are some limitation to the PAM matrices which makes the BLOSUM matrices somewhat more attractive. The dataset on which the initial PAM matrices were build is very old by now, and the PAM matrices assume that all amino acids mutate at the same rate - this is not a correct assumption.

BLOSUM
In 1992, 14 years after the PAM matrices were published, the BLOSUM matrices (BLOcks SUbstitution Matrix) were developed and published [Henikoff and Henikoff, 1992].

Henikoff et al. wanted to model more divergent proteins, thus they used locally aligned sequences where none of the aligned sequences share less than 62% identity. This resulted in a scoring matrix´called BLOSUM62. In contrast to the PAM matrices the BLOSUM matrices are calculated from alignments without gaps emerging from the BLOCKS database http://blocks.fhcrc.org/.

Sean Eddy recently wrote a paper reviewing the BLOSUM62 substitution matrix and how to calculate the scores [Eddy, 2004].